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Restructuring of Snapshots #429

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merged 68 commits into from Mar 3, 2016
Merged

Restructuring of Snapshots #429

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80e03de
support for arbitrary object type
jhprinz Nov 19, 2015
206ca90
support for arbitrary object type
jhprinz Nov 19, 2015
52b5037
Merge remote-tracking branch 'upstream/master' into addmultistore
jhprinz Nov 26, 2015
666b9b7
Merge remote-tracking branch 'upstream/master' into addmultistore
jhprinz Dec 2, 2015
1f742d5
Merge remote-tracking branch 'upstream/master' into addmultistore
jhprinz Dec 19, 2015
0cbabd1
Merge remote-tracking branch 'upstream/master' into dictstore
jhprinz Dec 20, 2015
c28535c
add cv as attribute feature
jhprinz Jan 4, 2016
e7ea055
doc update
jhprinz Jan 4, 2016
5742a5c
restructuring of CV
jhprinz Jan 4, 2016
cdaa588
restructuring of CV
jhprinz Jan 4, 2016
32c274c
simplification of CV
jhprinz Jan 4, 2016
8528014
save some disk space using better object description
jhprinz Jan 4, 2016
a205425
nb updates
jhprinz Jan 4, 2016
c7880b6
Merge branch 'newnaming' into engine_cv
jhprinz Jan 12, 2016
e3728c9
merge corrections
jhprinz Jan 12, 2016
1628887
toward better features
jhprinz Jan 20, 2016
337b620
compile __init__ and create_reversed
jhprinz Jan 21, 2016
d4d6c66
get features to work
jhprinz Jan 22, 2016
76ebe2c
cleanup of Snapshot constructor calling
jhprinz Jan 22, 2016
cf24ccd
speed up storage tests by simplifying topology
jhprinz Jan 22, 2016
88554e2
fixing nb
jhprinz Jan 22, 2016
ee6baf6
fixing nb
jhprinz Jan 22, 2016
2bd31be
Merge branch 'master' of github.com:choderalab/openpathsampling into …
jhprinz Jan 22, 2016
a712ea8
revert error in test
jhprinz Jan 22, 2016
07c7e84
remove necessity of is_reversed flag
jhprinz Jan 23, 2016
ecc6a26
add engine feature
jhprinz Jan 23, 2016
d7229cb
fix imports
jhprinz Jan 23, 2016
3a2b3ce
Merge branch 'netcdfdocs' into features
jhprinz Jan 23, 2016
0451279
better docstring generation
jhprinz Jan 25, 2016
1fc608b
Merge branch 'master' of github.com:choderalab/openpathsampling into …
jhprinz Jan 25, 2016
d94868a
Merge branch 'newnaming' into features
jhprinz Jan 25, 2016
44bb163
improve automatic docstring generation
jhprinz Jan 25, 2016
7d271e0
add feature shared for later
jhprinz Jan 25, 2016
09925a9
cleanup of snapshot_content
jhprinz Jan 25, 2016
ebee5c8
cleanup of snapshot_content
jhprinz Jan 25, 2016
8a86598
cleanup
jhprinz Jan 25, 2016
5a5cd97
Merge branch 'engine_cv' into featureengine
jhprinz Jan 25, 2016
e92d6c2
cleanup
jhprinz Jan 25, 2016
933669b
move Configuration and Momentum to features
jhprinz Jan 25, 2016
6b99c2b
docstring updates
jhprinz Jan 28, 2016
a3157fb
docstring updates
jhprinz Jan 28, 2016
ccdab74
code fixes
jhprinz Jan 28, 2016
3914c50
code fixes
jhprinz Jan 28, 2016
1a6c1ec
fix nosetests for removed function
jhprinz Jan 28, 2016
ea0ba27
fix nb
jhprinz Jan 28, 2016
df8b3f1
fix nb
jhprinz Jan 28, 2016
a7eb820
fix nb
jhprinz Jan 28, 2016
5529f43
fix nb
jhprinz Jan 28, 2016
297ec0b
fix nb
jhprinz Jan 28, 2016
55eed83
fix nb
jhprinz Jan 28, 2016
b42edb9
reduce runtime of alanine nb
jhprinz Jan 28, 2016
4f8c150
nb update
jhprinz Jan 28, 2016
14ab285
nb update
jhprinz Jan 28, 2016
8c65a31
merge branch 'master' of github.com:choderalab/openpathsampling into …
jhprinz Feb 9, 2016
45fd2b2
Merge branch 'master' of github.com:choderalab/openpathsampling into …
jhprinz Feb 10, 2016
9016403
add comments for Snapshot decorator
jhprinz Feb 25, 2016
f4ebbb8
Add docstring to NumpyDocTools
jhprinz Feb 25, 2016
1359e67
add utility function to create Snapshot classes
jhprinz Feb 25, 2016
09b8aab
add check for orthogonal features
jhprinz Feb 25, 2016
f028f01
little fixes
jhprinz Feb 25, 2016
d45c1bf
little changes as discussed in the PR
jhprinz Feb 29, 2016
8b7be04
little changes as discussed in the PR
jhprinz Feb 29, 2016
aa98aef
simplify treatment of _reversal Snapshot
jhprinz Mar 1, 2016
ed421c6
fix meta.yaml
jhprinz Mar 1, 2016
7dd873a
fix meta.yaml
jhprinz Mar 1, 2016
e77618b
little cleanup
jhprinz Mar 1, 2016
4fb4af2
little cleanup
jhprinz Mar 1, 2016
15aedf2
add analysis notebook for Snapshot class
jhprinz Mar 3, 2016
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2 changes: 1 addition & 1 deletion devtools/conda-recipe/meta.yaml
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Expand Up @@ -27,7 +27,7 @@ requirements:
- pymbar
- docopt
- pyyaml
- mdtraj
- mdtraj 1.5.1
- svgwrite
- networkx
- matplotlib
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